Listening to (and Saving) the World’s Languages. I don’t get why there are always “languages of the world are dying” articles popping up regularly in the mainstream and scientific media. I mean there’s a great benefit to having one language unify diverse groups. It’s just like how Europeans gained efficiencies by ditching their local currencies and going with the Euro. Eh, well, perhaps not the best example right now….

What can you learn from a whole genome sequence? Dr. Daniel MacArthur seems to suggest that there isn’t a whole lot more you can learn that you couldn’t learn from a chip with hundreds of thousands of SNPs instead of all 3 billion base pairs. Seems about right. And remember the baseline, many people are highly skeptical of the marginal value of the SNP chips beyond what you’d know from your family history.

…until the late 20th century the majority of the ancestry of the white population of the republic descended from those who were counted in the 1790 census.

A commenter questioned the assertion. The commenter was right to question it. My source was a 1992 paper that estimated that only in 1990 did the proportion of American ancestry which derived from those who arrived after the 1790 census exceeding 50%. In other words, if you ran the ancestors of all Americans back to 1790, a majority of that set would have been counted in the 1790 census (so people of mixed ancestry would contribute to the two components are weighted by their ancestry).
The major issue here is that there is a difference between whites, and non-whites, especially before mass Asian and Latin American immigration post-1965, when white vs. non-white ~ white vs. black. Almost all the ancestors of black Americans who were black were already resident in the United States in 1790. A few years ago I read up on the history of American slavery and was surprised how genuinely indigenous the black American, slave and free, population was by the late 18th century (English speaking and Christian). There was an obvious reason why Southern slave-holders went along with the ban on importation of slaves which was due to kick in in the early decades of the republic: American blacks, unlike slave populations elsewhere in the New World, had endogenous natural increase. This explains part of the relative paucity of African aspects in their culture in relation to the blacks of Haiti or Brazil, where African-born individuals were still very substantial numerically at emancipation because of high attrition rates (it is sometimes asserted that the majority of blacks liberated during the Haitian Revolution were born in Africa. Likely a hyperbole, but it gets across the strength of connection).

In any case, to estimate the white proportion attributable to 1790, I have to correct for the black proportion within the total. As an approximation I think it’s acceptable to simply attribute blacks as a whole to the proportion which had ancestors here in 1790 in full. I suspect a greater proportion of the black ancestry which post-dates 1790 would come from the white component of their heritage which simply isn’t of notice in American society for various reasons in any case (Henry Louis Gates Jr. is more white than he is black in terms of ancestry, but he’s the doyen of Africana Studies). So, assuming that blacks contribute to the 1790 and before component in full, I estimate that between 1910 and 1920 the majority of the ancestry of the white population shifted from 1790 and before, to after. Specifically, in 1910 51% of the ancestry could be traced to 1790 and before among whites, and in 1920 49%. In 1950 it was 47% 1790 and before. So I should have said early 20th century, not late. I wouldn’t be surprised though if the balance has started to shift in recent years, as many “white ethnic” groups (Jews, Italians, Irish, etc.) are more heavily concentrated in urban areas, while the most fertile white community in the United States, the Mormons of Utah, are also the most Old Stock Yankee in ancestry (I am aware that many Mormons are descended from European immigrants who converted in Europe and made the journey after conversion, but Mormons are still far more Old Stock Yankee than any group outside of interior New England).

I am currently reading Peter Heather’s Empires and Barbarians: The Fall of Rome and the Birth of Europe. This is a substantially more hefty volume in terms of density than The Fall of the Roman Empire: A New History of Rome and the Barbarians . It is also somewhat of a page turner. One aspect of Heather’s argument so far is his attempt to navigate a path between the historically tinged fantasy of what its critics label the “Grand Narrative” of mass migration of barbarian tribes such as the Goths, Vandals and Saxons during the 4th to 6th centuries, dominant before World War II, and its post-World World II counterpoint. As a reaction against this idea archaeologists have taken to a model of pots-not-people, whereby cultural forms flow between populations, and identities are fluid and often created de novo. This model would suggest that only a tiny core cadre of “German” “barbarians” (and yes, often in this area of scholarship the most banal terms are problematized and placed in quotations!) entered the Roman Empire, and the development of a Frankish ruling class in the former Gaul, for example, was a process whereby Romans assimilated to the Germanic identity (with the shift from togas to trousers being the most widespread obvious illustration of Germanization of norms). I believe that liberally applied this model is fantasy as well. Being a weblog where genetics is important, my skepticism of both extreme scenarios is rooted in new scientific data.

There are cases, such as the Etruscans, where the migration is clear from the genetics, both human and their domesticates. The peopling of Europe after the last Ice Age is now very much an open question. The likelihood that the present population of India is the product of an ancient hybridization event between an European-like population and an indigenous group with more affinity with eastern, than western, Eurasian groups, is now a rather peculiar prehistoric conundrum. It also seems likely that the spread of rice farming in Japan was concomitant with the expansion of a Korea-derived group, the Yayoi, at the expense of the ancient Jomon people. And yet there are plenty of inverse cases. The spread of Latinate languages and Romanitas did not seem to perturb the basic patterns of genetic relationship among the peoples of Europe. The emergence of the Magyar nation on the plains of Roman Pannonia seems to have involved mostly the Magyarization of the local population. In contrast, the Bulgars were totally absorbed by their Slavic subjects culturally, leaving only their name. The spread of the Arabic language and culture was predominantly one of memes, not genes (clearly evident in the current dynamic of Arabization in parts of the Maghreb).

And yet you will note that there is a slight difference between the few examples I’ve cited: population replacement seems to have occurred in the more antique cases, rather than the more recent ones. This would naturally bias the perspectives of historians, who have much more data on more recent events (no offense, but archaeologists seem to be able to say whatever they want!). The Etruscan language itself is known only from fragments, while the happenings in prehistoric Europe and India can only be inferred very indirectly. I now offer a modest hypothesis for the distinction, why in some cases is it just the “pots” which move (Arabs), and in other cases it is the people who move (the Japanese). In cases of population replacement there is often a shift in mode of production. In cases where there is the diffusion of culture it is often a system or set of ideas which rent-seeking elites can exploit to maintain their position, or perpetuate it, flow across space. Islam was not only a potent ideology which bound the tribes of Arabia together so that they could engage in collective action, local elites across the new Muslim-dominated world found it a congenial international system whereby they could integrate themselves into a civilization of elite peers, as well as justify their god-given position at the apex of the status hierarchy (granted, many had this in the form of Christianity or Zoroastrianism, but once the old top dogs were overthrown the benefit of these systems was considerably less). The spread of Yayoi culture in Japan involved a shift from more extensive, toward more intensive, forms of agriculture. Their population base was greater, and the domains of the Jomon were left “underexploited” from the perspective of the more productive mode of agriculture which the Yayoi were engaged in. It need not be an issue of mass slaughter or extermination, a high endogenous rate of natural increase as well as disease, combined with assimilation and co-option of local elites, could result in the swallowing up of a population engaged in a less intensive mode of production. This sort of hybrid aspect of cultural and genetic expansion, whereby the local substrate is assimilated and synthesized with the expanding ethnic group, seems to be a good fit to the pattern that we see among the Han of China.

But shifts from modes of production exhibit some level of discontinuity, insofar as there are diminishing returns once all the land appropriate for that mode of production has been taken over. Farmers who are expanding into land held by hunter-gatherers or those practicing less intensive forms of agriculture can have enormous rates of natural increase because they’re not bound by Malthusian constraints. This is evident in the United States, until the late 20th century the majority of the ancestry of the white population of the republic descended from those who were counted in the 1790 census. The reason had to do with the extremely high birthrates among white Americans. When regions such as New England were “filled up,” they pushed out to the “frontier,” to northern Ohio, then to the Upper Midwest, and finally the Pacific Northwest. And in the process there was a radical change in the genetic variation of North America, as the indigenous populations died from disease, were numerically overwhelmed, or genetically absorbed. This is an extreme case scenario, but I think it illustrates what occurs when modes of production collide, so to speak. The pattern in Latin America was somewhat different, though an amalgamated Mestizo population did emerge over time, there was not the wholesale demographic replacement in many regions. And I believe that the reason is that the Iberians did not bring a superior mode of production, rather, the large local population base engaged in agriculture presented an opportunity for rent-seekers to place themselves atop the status hierarchy. Sometimes this involved intermarriage with local elites, as was the case in Peru where the nobility of the Inca intermarried with the Spanish conquistadors for the first few generations (the whiteness of the Peruvian elite despite the fact that the old families have Inca ancestry is simply due to dilution as successive generations of lower Spanish nobility set off to the New World and married into Creole families).

By the Roman period I believe that much of the core Old World was “filled up” in terms of intensive agricultural production. So most, though not all, of the changes in ethnicity or identity are biased toward elite emulation and novel identity formation. The Turks did not bring an innovative new economic system whereby they replaced the Greek and Armenian peasantry in Anatolia, rather, on the contrary peculiarities in the Turkish Ottoman system of rule produced a situation where the old families were usually replaced in positions of power by converts from the Christian groups who assimilated to a Turkish identity. When the economic arrangements reach stasis and the population is at Malthusian equilibrium change is a matter of shifting identities and affinities of the rent-seekers. When radically new economic systems emerge, opportunities for disparate population growth present themselves. Ergo, England went from being demographically dwarfed by France in the 17th century, to surpassing it in population in the 19th. England was of course the first nation to break into a new mode of production since the agricultural revolution.

Credit: Thanks to Michael Vassar for triggering this line of reasoning after a conversation we had about the Neolithic revolution.

Comments Off on Men & ideas on the move: settled lands & colonized minds

A few months ago I blogged a paper in PLoS Biology which suggested that a common Y chromosomal haplogroup, in fact the most common in Europe and at modal frequency along the Atlantic fringe, is not pre-Neolithic. Rather their analysis of the data implied that the European variants were derived from an Anatolian variant. The implication was that a haplogroup which had previously been diagnostic of “Paleolithicness,” so to speak, of a particular population may in fact be an indication of the proportion of Neolithic Middle Eastern ancestry. The most interesting case were the Basques, who have a high frequency of this haplogroup, and are often conceived of as “ur-Europeans,” Paleolithic descendants of the Cro-Magnons in the most romantic tellings. I was somewhat primed to accept this finding because of confusing results from ancient DNA extraction which implies a lot of turnover in maternal lineages, the mtDNA. My logic being that if the mtDNA exhibited rupture, then the Y lineages should too, as demographic revolutions are more likely to occur among men.

Two alternative models have been proposed to explain the spread of agriculture in Europe during the Neolithic period. The demic diffusion model postulates the spreading of farmers from the Middle East along a Southeast to Northeast axis. Conversely, the cultural diffusion model assumes transmission of agricultural techniques without substantial movements of people. Support for the demic model derives largely from the observation of frequency gradients among some genetic variants, in particular haplogroups defined by single nucleotide polymorphisms (SNPs) in the Y-chromosome. A recent network analysis of the R-M269 Y chromosome lineage has purportedly corroborated Neolithic expansion from Anatolia, the site of diffusion of agriculture. However, the data are still controversial and the analyses so far performed are prone to a number of biases. In the present study we show that the addition of a single marker, DYSA7.2, dramatically changes the shape of the R-M269 network into a topology showing a clear Western-Eastern dichotomy not consistent with a radial diffusion of people from the Middle East. We have also assessed other Y-chromosome haplogroups proposed to be markers of the Neolithic diffusion of farmers and compared their intra-lineage variation—defined by short tandem repeats (STRs)—in Anatolia and in Sardinia, the only Western population where these lineages are present at appreciable frequencies and where there is substantial archaeological and genetic evidence of pre-Neolithic human occupation. The data indicate that Sardinia does not contain a subset of the variability present in Anatolia and that the shared variability between these populations is best explained by an earlier, pre-Neolithic dispersal of haplogroups from a common ancestral gene pool. Overall, these results are consistent with the cultural diffusion and do not support the demic model of agriculture diffusion.

Their main trump cards seem to be that they used a denser set of markers, and, they claim they have a more accurate molecular clock. Ergo, in the latter case they produce a better time to the last common ancestor, which is twice as deep as the paper they’re attempting to refute. Someone like Dienekes or Polish Genetics can tackle the controversies in scientific genealogy here (I know Dienekes has a lot of interest in mutational rates which go into the molecular clock for these coalescence times). Rather, I would suggest that usage of Sardinians concerns me for an obvious reason: they’re genetic outliers in Europe. A lot of this has to do with being an island. Islands build up uniqueness because they don’t engage in the normal low level gene flow between adjacent populations because they’re…well, islands. You would know about Sardinia’s position because they’re one of the populations in L. L. Cavalli-Sforza’s HGDP sample and they show up in History & Geography of Human Genes as on the margins of the PCA plots. But here’s a figure from a more recent paper using a much denser market set, constrained to Southern European populations. I labelled some of the main ones so you’d get a sense of why I say Sardinians are outliers:

Over the two largest independent dimensions of genetic variation you can see a distribution from the southeast Mediterranean all the way to the northwest (in fact, the Basques are an Atlantic group). The Sardinians are out of the primary axis, and that’s why I say they’re an outlier. A few other European groups, like the Icelanders and Sami exhibit this tendency. As I suggested above I think the fact that the Sardinians are on an isolated island relatively far from the European and Africa mainland means that they’ll “random walk” in genetic variation space toward an outlier status naturally, just as the Icelanders have since the year 1000. So though I grant the authors their rationale for using the Sardinians as a reference against the Anatolian source population, the fact that we know that they’re peculiar in their variation in total genome content makes me wary of drawing too many inferences from their relationships to other groups where they are seen as representative of a larger set.

Citation:Morelli L, Contu D, Santoni F, Whalen MB, & Francalacci P (2010). A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture PLoS ONE : 10.1371/journal.pone.0010419

Experiments in cultural transmission and human cultural evolution. I’ve read plenty of models of cultural evolution (Cavalli-Sforza & Feldman, Boyd & Richerson, come to mind), but a post which reviews some more empirical literature. One criticism of modelers of cultural evolution is that they’re all talk, no action, and so basically just mathed up versions of armchair humanists.

Wired for Sex. The existence of two sexes is of obvious evolutionary genetic interest; males are an “expensive” cost for a lineage. But obviously there are other angles to explore, including neurological. Because sexual dimorphism takes a while to evolve I think one possible way to get a good grip on sex differences in the brain might be to look at male vs. female anatomy, function and neuochemistry across the great apes + humans. Presumably many of the differences are basal characteristics.

Can’t Pivot to the Economy With Magic. I disagree. It’s a world filled with magic & mystery, we need to just open our eyes and appreciate it. We can can use magic & mystery as fuel to generate productivity gains. A wizard in every home I say!

A Connecticut woman who had a voluntary double mastectomy after genetic testing is alleging her employer eliminated her job after learning she carried a gene implicated in breast cancer.

Pamela Fink, 39, of Fairfield said in discrimination complaints that her bosses at natural gas and electric supplier MXenergy gave her glowing evaluations for years, but targeted, demoted and eventually dismissed her when she told them of the genetic test results.

Her complaints, filed Tuesday with the U.S. Equal Opportunity Commission and Connecticut Commission on Human Rights and Opportunities, are among the first known to be filed nationwide based on the federal Genetic Information Nondiscrimination Act.

What probability do readers put in regards to this being a legitimate complaint? This seems a large firm, so I doubt that group insurance rates would change because of one person (I have heard of this occurring in small businesses where an expensive employee or employee’s family member can effect the rate for everyone else). So if it is legitimate the main issue would have been their fear of future illness, but the woman in question went through a double mastectomy, which I assume would obviate that concern. What am I missing? Are there expectations that she’d be taking medical leave in the future due to follow up operations or treatment?

Change is quite in the air today, whether it be climate change or human induced habitat shifts. What’s a species in the wild to do? Biologists naturally worry about loss of biodiversity a great deal, and many non-biologist humans rather high up on Maslow’s hierarchy of needs also care. And yet species loss, or the threat of extinction, seems too often to impinge upon public consciousness in a coarse categorical sense. For example the EPA classifications such as “threatened” or “endangered.” There are also vague general warnings or forebodings; warmer temperatures leading to mass extinctions as species can not track their optimal ecology and the like. And these warnings seem to err on the side of caution, as if populations of organisms are incapable of adapting, and all species are as particular as the panda.

Many species are experiencing sustained environmental change mainly due to human activities. The unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. To begin to understand the limits to population persistence, we present a simple evolutionary model for the critical rate of environmental change beyond which a population must decline and go extinct. We use this model to highlight the major determinants of extinction risk in a changing environment, and identify research needs for improved predictions based on projected changes in environmental variables. Two key parameters relating the environment to population biology have not yet received sufficient attention. Phenotypic plasticity, the direct influence of environment on the development of individual phenotypes, is increasingly considered an important component of phenotypic change in the wild and should be incorporated in models of population persistence. Environmental sensitivity of selection, the change in the optimum phenotype with the environment, still crucially needs empirical assessment. We use environmental tolerance curves and other examples of ecological and evolutionary responses to climate change to illustrate how these mechanistic approaches can be developed for predictive purposes.

Their model here seems to be at counterpoint to something called “niche modelling” (yes, I am not on “home territory” here!), which operates under the assumption of species being optimized for a particular set of abiotic parameters, and focusing on the shifts of those parameters over space and time. So extinction risk may be predicted from a shift in climate and decrease or disappearance of potential habitat. The authors of this paper observe naturally that biological organisms are not quite so static, they exhibit both plasticity and adaptiveness within their own particular life history, as well as ability to evolve on a population wide level over time. If genetic evolution is thought of as a hill climbing algorithm I suppose a niche model presumes that the hill moves while the principal sits pat. This static vision of the tree of life seems at odds with development, behavior and evolution. The authors of this paper believe that a different formulation may be fruitful, and I am inclined to agree with them.

As I observed above the formalism undergirding this paper is exceedingly simple. On the left-hand side you have the variable which determines the risk, or lack of risk, of extinction more or less, because it defines the maximum rate of environmental change where the population can be expected to persist. This makes intuitive sense, as extremely volatile environments would be difficult for species and individual organisms to track.Too much variation over a short period of time, and no species can bend with the winds of change rapidly enough. Here are the list of parameters in the formalism (taken from box 1 of the paper):

ηc – critical rate of environmental change: maximum rate of change which allows persistence of a population

B – environmental sensitivity of selection: change in the optimum phenotype with the environment. It’s a slope, so 0 means that the change in environment doesn’t change optimum phenotype, while a very high slope indicates a rapid shift of optimum. One presumes this is proportional to the power of natural selection

T – generation time: average age of parents of a cohort of newborn individuals. Big T means long generation times, small T means short ones

σ2 – phenotypic variance

h2 – heritability: the proportion of phenotypic variance in a trait due to additive genetic effects

rmax intrinsic rate of increase: population growth rate in the absence of constraints

b – phenotypic plasticity: influence of the environment on individual phenotypes through development. Height is plastic; compare North Koreans vs. South Koreans

γ – stabilizing selection: this is basically selection pushing in from both directions away from the phenotypic optimum. The stronger the selection, the sharper the fitness gradient. Height exhibits some shallow stabilizing dynamics; the very tall and very short seem to be less fit

Examining the equation, and knowing the parameters, some relations which we comprehend intuitively become clear. The larger the denominator, the lower the rate of maximum environmental change which would allow for population persistence, so the higher the probability of extinction. Species with large T, long generation times, are at greater risk. Scenarios where the the environmental sensitivity to selection, B, is much greater than the ability of an organism to track its environment through phenotypic plasticity, b, increase the probability of extinction. Obviously selection takes some time to operate, assuming you have extant genetic variation, so if a sharp shift in environment with radical fitness implications occurs, and the species is unable to track this in any way, population size is going to crash and extinction may become imminent.

On the numerator you see that the more heritable variation you have, the higher ηc. The rate of adaptation is proportional to the amount of heritable phenotypic variation extant within the population, because selection needs variance away from the old optimum toward the new one to shift the population central tendency. In other words if selection doesn’t result in a change in the next generation because the trait isn’t passed on through genes, then that precludes the population being able to shift its median phenotype (though presumably if there is stochastic phenotypic variation from generation to generation it would be able to persist if enough individuals fell within the optimum range). The strength of stabilizing selection and rate of natural increase also weight in favor of population persistence. I presume in the former case it has to do with the efficacy of selection in shifting the phenotypic mean (i.e., it’s like heritability), while in the latter it seems that the ability to bounce back from population crashes would redound to a species’ benefit in scenarios of environmental volatility (selection may cause a great number of deaths per generation until a new equilibrium is attained).

Of course a model like the one above has many approximations so as to approach a level of analytical tractability. They do address some of the interdependencies of the parameters, in particular the trade-offs of phenotypic plasticity. In this equation 1/ω2b quantifies the cost of plasticity, r0 represents increase without any cost of plasticity. We’re basically talking about the “Jack-of-all-trades is a master of none” issue here. In a way this crops up when we’re talking of clonal vs. sexual lineages on an evolutionary genetic scale. The general line of thinking is that sexual lineages are at a short-term disadvantage because they’re less optimized for the environment, but when there’s a shift in the environment (or pathogen character) the clonal lineages are at much more risk because they don’t have much variation with which natural selection can work. What was once a sharper phenotypic optimum turns into a narrow and unscalable gully.

Figure 2 illustrates some of the implications of particular parameters in relation to trade-offs:

There’s a lot of explanatory text, as they cite various literature which may, or may not, support their model. Clearly the presentation here is aimed toward goading people into testing their formalism, and to see if it has any utility. I know that those who cherish biodiversity would prefer that we preserve everything (assuming we can actually record all the species), but reality will likely impose upon us particular constraints, and trade-offs. In a cost vs. benefit calculus this sort model may be useful. Which species are likely to be able to track the environmental changes to some extent? Which species are unlikely to be able to track the changes? What are the probabilities? And so forth.

I’ll let the authors conclude:

Our aim was to describe an approach based on evolutionary and demographic mechanisms that can be used to make predictions on population persistence in a changing environment and to highlight the most important variables to measure. While this approach is obviously more costly and time-consuming than niche modelling, its results are also likely to be more useful for specific purposes because it explicitly incorporates the factors that limit population response to environmental change.

The feasibility of such a mechanistic approach has been demonstrated by a few recent studies. Deutsch et al…used thermal tolerance curves to predict the fitness consequence of climate change for many species of terrestrial insects across latitudes, but without explicitly considering phenotypic plasticity or genetic evolution. Kearney et al…combined biophysical models of energy transfers with measures of heritability of egg desiccation to predict how climate change would affect the distribution of the mosquito Aedes aegiptii in Australia. Egg desiccation was treated as a threshold trait, but the possibility of phenotypic plasticity or evolution of the threshold was not considered. These encouraging efforts call for more empirical studies where genetic evolution and phenotypic plasticity are combined with demography to make predictions about population persistence in a changing environment. The simple approach we have outlined is a necessary step towards a more specific and comprehensive understanding of the influence of environmental change on population extinction.

April 28, 2010

On paper, that’s what Sudan’s 21-year civil war was all about. More than 2 million people died in that terrible religious-themed conflict between the Muslim, Arab-led north and the pagan and Christian black south. In reality, almost no one in the south bought the unity line except their charismatic (and autocratic) leader, John Garang. Garang, a favorite of the West, negotiated Sudan’s 2005 peace treaty, the Comprehensive Peace Agreement, that finally ended the war. The document was essentially written to ensure he would be elected Sudan’s first black president.

How is it that the current president of Sudan (picture to the left) isn’t black, but Barack Hussein Obama is black? I’m in the category of people who think the world “race” has some utility and maps onto real patterns of human variation, but sometimes it’s just funny. The distinction between the Arabs of Sudan and blacks of Sudan is kind of weird, because Arab is not a race, and Arabs can be of any race theoretically (there are even Arabs in Yemen’s Hadhramaut who have a lot of Malaysian ancestry because of international trade), though generally they are of the olive persuasion. Perhaps the Sudanese Arab elite wouldn’t want to be identified as black because that isn’t particularly prestigious, but they’d certainly be identified as such in other Arab countries. Anwar Sadat was the subject of some racist attitudes within Egyptian society because of his Sudanese ancestry (his mother was Nubian) and his dark skin.

Anyway, my amusement was mostly the fact that they went with this text, and, added a picture of a man who most Americans would identify as black but noted implicitly that he wasn’t black. American journalists are generally punctilious about following the rule of hyodescent when it comes to Americans, even when those individuals object to this framing, such as Tiger Woods (who is twice as Asian ancestrally as he is black). But I guess in an international context they will bend more. It reminded me of stories that Afro-Arabs were often allowed to stay at “whites only” facilities in the USA when segregation was the norm because they were foreign.

Note: Hypodescent isn’t just an American issue. There are controversies about a new biopic of Alexandre Dumas where he is played by Gérard Depardieu. Some people wanted a non-white actor cast because Dumas’ mother was mixed-race. But of course Dumas was mostly white, and he seems to basically have looked like a white guy. France of the 19th century was not the American South of the 19th century, and a drop of black blood did not make you persona non grate within white society. If you want real accuracy, perhaps cast Wentworth Miller as a young Dumas, he’s a white-looking mixed-race actor.

I listened today to an interview with Stephen Prothero, which outlined the argument in his book God Is Not One: The Eight Rival Religions That Run the World-and Why Their Differences Matter. Prothero is a professor in the Department of Religion at Boston University, and he certainly brings some heft to this argument. Not having read the book, but listening to his talking points in interview and discussion, he seems to have a problem as an empirical matter with the contention regularly made in interfaith circles that all religions fundamentally point to the same truth. The metaphor that Houston Smith used whereby religions are separate paths to the same mountain top is referred to repeatedly. Prothero suggests that this universalistic model denies the deep reality of sectarian difference in belief, practice and outlook, and tends to be favored by those of liberal bent at ease with multiculturalism. He also notes that the foundation of common unity can be traced back to the perennial philosophy. This philosophy lay at the heart of the Traditionalist School, of which Smith was arguably a member, as was Julius Evola. So the tendency that Prothero is putting into focus is not necessarily associated with liberalism, though in the American context it is because of the Right’s capture by low church anti-elitist elements.
An illustration of the problems which crop up when those of distinctive religions attempt to find common ground is that that commonality is often generated through an exclusion of an out group. Jews, Muslims and Christians all worship the God of Abraham. But of course Buddhists find the God of Abraham irrelevant to the central questions of religion. Prothero also observes that liberal universalism tends to put a premium on elite mysticism, a mode of religiosity which is notable for transcendence of sectarian distinctions. But the much more common mode of religious life is that of plain believers who take distinctive beliefs and practices rather seriously. Pragmatically this sort of consideration is critical when assessing whether a Sunni vs. Shia distinction will have any importance. At the level of Sufi mystics these distinctions may melt away, but the rest of humanity is still something one must consider if one is a more prosaic sort who does not expect to actively gain salvation before death.

And it is at the level of the rest of humanity that I think Prothero’s own methodological orientation may cause problems in interpreting the world as it is. From what I can tell he operates out of the framework of Religious Studies (which coincidentally in the United States was shaped by Mircea Eliade, who was strongly influenced by Traditionalism). Too often it seems to me that scholars out of this tradition operate as if religion is a concrete entity, distinct and unique, as opposed to being an emergent property of normal aspects of culture and cognition. It is scientists who start from a naturalistic perspective who I think can take a final step back, and see religion as but a piece of the painting. Prothero is correct obviously that adherents of different religions view themselves as distinct, as following different truths. Fundamentalist Christians are liable to dismiss Allah as an Arab pagan divinity, or even a demon, despite the widely held belief by many that Allah is simply a different name for the God of the Christians. But what if you don’t believe that gods exist except in the minds of believers? Then whether as a practical fact Allah and the Christian God Allah or Lord Buddha are distinct beings rests in large part on whether humans conceptualize them differently. It turns out that in general they do not. In other words religious believers tend to conceive of their supernatural agents very similarly, whose traits are rather interchangeable, with the main difference being semantic. The book Theological Incorrectness cites a wide range of literature in this area, with a particular reference to the religious landscape of Sri Lanka.

The disjunction between assertions and sincere beliefs of deep difference, and the reality that cognitively there’s little gap at all, shouldn’t be too surprising. Promiscuity of belief has been relatively normal for much of human history, as was evident in the pre-Christian Roman Empire, or is evident in Japan or China. The exclusive tribal aspect of Islam and Christianity combined with their universal ambitions are somewhat atypical, though this suite of characters has been highly successful in propagating itself. Additionally, religion is more than simply belief, it is about communal rituals and belonging, and the daily regularity of banal practices and customs. Prothero is correct that acknowledging the deep differences are important, but I believe to a great extent he is wrong as to what those differences are. That Buddhism emphasizes suffering while Christianity emphasizes sin is not particularly significant unless you’re a Buddhist or a Christian, and even then most Christians have no idea what soteriology means for example. Beliefs are shallow markers to group affiliations, not deeply held axioms which serve as starting lines for chains of inference. Religious elites construct many distinctive aspects of their brand, but it is the functional components which are essential in furthering community and human flourishing.

I think the Shia-Sunni split which Stephen Prothero gives as an example of the need to understand the depths of difference is a good case of how beliefs may be secondary. The division here began originally as a political dispute, whereby the partisans of Ali and his family dissented from the decisions of the Muslim majority in the succession to the position of Caliph. Over the centuries these partisans evolved into the Shia faction, while those who were not Shia or other assorted sectarians become Sunni. Some distinctions of practice and belief did arise across this divide, but in general those distinctions evolved after the original political division (because the Shia party was decentralized they have preserved more of the theological diversity of early Islam than the Sunnis).

On a deep level Huston Smith was right. Human psychology is universal, so human intuitions about supernatural aspects of the world exhibit deep commonality and intelligibility. But it really doesn’t matter, human tribalism is also a universal, and it co-opts these religious intuitions into its service. The fact that both tribes don tattoos does not elicit in them an appreciation of the universality of these sorts of markers, the importance of belonging. Rather, the markers often separate those who are your brothers, and those who you wish to kill. In other words, what you believe may matter less than what you believe about what you believe.

Comments Off on God is none, but it does matter

April 27, 2010

Angst on the Aegean. Like many Third World countries Greece is characterized by familialism and rampant corruption typical of a low trust society (more on the familialism). Except thanks to geography Hellenes are like a boat being lifted by the rising tide of the dynamic economies of other European nations (the reason Mexico has a GDP PPP per capita of $15,000 and Colombia $9,000 probably has something to do the former’s more favorable location). Greek culture and government seems trapped in a particularly unfortunate equilibrium, and the buck stops soon. I have mooted that perhaps many nations in this position might benefit from the importation of a Suomalaiset bureaucratic class to “shock” the society to another state where virtuous circles of trust may arise. Such a mandarin caste would be congenitally incapable of eye contact, minimizing the ability to weasel out bribes.

“Save A Mother”: An Appeal. My friend Ruchira Paul is trying to raise money for a charity focused on Indian rural maternal health after she got to know the doctor who heads it. You can find out more here.

A few weeks ago I reviewed a paper on the the genetics of the Cape Coloured population. Within it there was a refrence to another paper, Deconstructing Jaco: genetic heritage of an Afrikaner. The title refers to the author himself. It was an analysis of his own pedigree going back to the 17th century, along with his mtDNA, his father’s mtDNA, and his Y lineage. The genetics is a bit thin, but the pedigree information is of Scandinavian quality from what I can tell. Praised the records of the Reformed Church!

The author’s utilizes an inversion of the typical method whereby a survey of a population may give some insight into individuals within that population. Rather, he leverages the thorough church records of his Afrikaner community, and his local roots, to paint a picture of his own ancestry. Then he compares the results to those of the community as a whole. Though an N of 1 certainly has limits it seems that the author concludes that he is relatively representative because some of the statistics that emerge out of pedigree analysis seem to fall in line with what genealogists working with the whole community have found. Additionally, it is clearly that he has deep roots within the historic Afrikaner nation, so assuming random mating and little population substructure, inferences from his pedigree may have some general utility.

Afrikaners apparently have some peculiarities genetically which has made them of some interest to scientists. It turns out that they seem to exhibit high frequencies of classical Mendelian diseases, a hallmark of inbreeding or population bottlenecks. This aligns well with the thesis that Afrikaners are the descendants of a small group of founders who arrived in the 17th century and entered into a long phase of demographic expansion, which culminated with their long Trek into the veld to escape English domination as well as perpetuate their practice of slavery (James Michner’s The Covenant is a fictionalization of this). As I have observed before the primacy of the “first settler” seems to loom large in the minds of demographers.

J. M. Greef, the author of the above paper, seems to refute this simple story in his own genealogy, though not the core aspect of the importance of the first founders. First the abstract:

It is often assumed that Afrikaners stem from a small number of Dutch immigrants. As a result they should be genetically homogeneous, show founder effects and be rather inbred. By disentangling my own South African pedigree, that is on average 12 generations deep, I try to quantify the genetic heritage of an Afrikaner. As much as 6% of my genes have been contributed by slaves from Africa, Madagascar and India, and a woman from China. This figure compares well to other genetic and genealogical estimates. Seventy three percent of my lineages coalesce into common founders, and I am related in excess of 10 times to 20 founder ancestors (30 times to Willem Schalk van der Merwe). Significant founder effects are thus possible. The overrepresentation of certain founder ancestors is in part explained by the fact that they had more children. This is remarkable given that they lived more than 300 years (or 12 generations) ago. DECONSTRUCT, a new program for pedigree analysis, identified 125 common ancestors in my pedigree. However, these common ancestors are so distant from myself, paths of between 16 and 25 steps in length, that my inbreeding coefficient is not unusually high (f approximately 0.0019).

Inbreeding coefficient is the probability that one’s two alleles are identical by descent. That is, they come from the same individual. For example, in the case of Elisabeth Fritzl her children have many genes where the alleles are identical by descent because half of her own genes are from her father, some many of his alleles will come back to reside within the same individual as part of a diploid pair. J. M. Greef notes that his inbreeding coefficient is about twice as high as is the norm for the typical European. Europe is a region of relatively low consanguinity, so this is a stringent reference. In some populations the inbreeding coefficient can be as high as 0.01. In short, he’s not too inbred.

That being said, the data within his pedigree do seem to show disproportionate contribution by some ancestors. This makes sense for two primary reasons. First, some component of reproductive variance is random (often modeled as a poisson distribution). Second, some component of reproductive variance is due to innate fitness (e.g., the Genghis Khan Y haplotype may be a case of this). Equality of contribution just isn’t in the cards.

Figure 2 shows the distribution of relationships within the pedigree:

Panel a illustrates that one individual is an ancestor of the author 30 times over! Many individuals are ancestors only once. Panel b shows relatedness, and again, some individuals are much closer to the author than others, with a skewed distribution. Panel c shows the number of generations between the ancestor and the author. The median number is well above ten generations, so the author has deep roots in South Africa. Finally, panel d shows the number of steps between his parents for any given ancestor. Because the author’s parents are both Afrikaners they share many common ancestors, but the steps between seem relatively large, and confirms that the author is not particularly inbred (if the parents were first cousins naturally there would be much shorter steps to common ancestors). It is clear disproportionate amount of J. M. Greef’s genes come from early settlers. This makes sense insofar as demographic expansion was likely front loaded, with later settlers having less of a chance to make an impact on an already large population.

The following table shows the contribution by various European and non-European groups to the author’s ancestry, as well as estimates for the total Afrikaner population in earlier studies on the right.

Note one point: only a minority of the ancestry of the author and Afrikaners are ethnically Dutch. This is important, because it shows how culture can spread and overwhelm ancestry. The Dutch imposed their language upon the French Huguenots, and their religion upon the Germans (who I presume were mostly Lutheran if they were from northern Germany, though a minority were Reformed or Catholic surely). Obviously the Reformed Calvinist religion and Afrikaans language both have a unique stamp in South Africa, but the connection of the Afrikaners to the Netherlands remained profound rather late in history. The Prime Minister of South Africa from 1958-1966 was born in the Netherlands. And yet another fact hard to deny is that the Huguenot French component seems to have persevered to a greater extent culturally than the German. The last Afrikaner President was named F. W. de Klerk, his surname being a form of Le Clerc. Another prominent South African head of state was Daniel Francois Malan. The author observes:

It is not clear if my higher estimate of French contribution is because of a systematic mistake in Heese’s (1970) estimate, or if it is because of a quirkiness in my own ancestry. It seemed to be the case that when a lineage hit the French Huguenots it stayed in this group. It will be interesting to compare the degree of inbreeding of the early generations of Huguenots to the other early immigrants. In the light of the calculations of Heyer et al. (2005) there is an interesting possibility that the cultural inheritance of fitness may have led to a systematic bias in Afrikaners, since Huguenots tended to be more educated and trained than German emigrants who tended to be soldiers. We are currently investigating this hypothesis.

There is a joke that the Baltic possessions of the Swedish monarchy were conquered with Finnish soldiers. Similarly, the Dutch overseas colonial possessions were staffed, especially at a lower level, by the rural male population surplus of northern Germany. A great many of these, likely the vast majority, never returned home and died abroad. These men contributed greatly to the census size of the Afrikaner population during much of its history, but it seems plausible that their fitness was far lower than the established Dutch and Huguenot groups because they lacked the resources and capital to flourish in a world which was much closer to the Malthusian edge than today. Many people don’t leave descendants, and it seems plausible that these Germans were fated not to do so to a far greater extent than the Dutch and Huguenots whom they were employed to protect and serve. Because of the genetic closeness of the north German and Dutch populations (in reality, Dutch are really simply another group of north Germans who transformed their regional identity into a national one for various reasons) I doubt that more thorough genetic testing will resolve this, rather, more pedigree analysis needs to be done on other individuals. But it’s an insight into the fact that social parameters have often been crucial to fitness in the human past.

As for the non-white component, the author’s results match those of previous researchers. He confirmed the likely probability of these results by the fact that his father carries mtDNA group M, which is most diverse in India. And in fact his father’s maternal lineage does trace back to a woman who was likely an Indian slave (slave women had particular surnames indicating their origin). My previous posts on the Coloureds highlighted the large Asiatic component to their ancestry, and it looks like previous researchers ignored this and focused on the Khoisan and Bantu. They also attempted to calculate ancestry based on classical markers which were found in African populations, and are present in low frequencies in Afrikaners, but that might ignore Asian signature markers (additionally, I assume that there was some natural selection for G6PD alleles). A survey of the total genomes of Afrikaners should be able to resolve the details of their ancestry, but it seems that the Afrikaners are far more colored than white Americans, by a factor of 5, but far less than white Latin Americans like Argentineans, probably by a factor of 5.

Finally, the author was also able to assess whether his ancestors exhibited a trade between quantity and quality in terms of their optimal number of offspring. In other words, did those who favored an extreme r or K selected strategy suffer vis-a-vis those who produced a more moderate number of offspring, not too low, and not too high? The author did not find any evidence of a tradeoff, and an optimal fitness. He was careful not to generalize too much, especially in light of the fact that Dutch colonial South Africa was an atypical society in many ways. I assume that living on the frontier means not having to say you’re sorry if you breed too much or too little.

Last week I was emphasizing the fact that someone from Max Planck seemed to really be positive about the University of New Mexico research which indicates that there has been “archaic” admixture into the modern human lineage derived from Out-of-Africa. This was curious because Svante Pääbo is at the Max Planck Institute, and he’s reconstructing the Neandertal genome. I wasn’t going to do more than hint at rumors, so I’ll point to Thomas Mailund (after linking to posts on the topic of admixture or not) :

I really look forward to reading the Neandertal paper and see what it has to say about gene flow between us and Neandertals. A few month ago, while I visited his group in Leipzig, Svante Pääbo actually promised to show me the draft, but it never happened. In Ohio in February I talked to one of the authors on the paper and he wouldn’t reveal anything… I guess I just have to wait and can only hope that it won’t be too long.

Remember that I didn’t say anything, Thomas Mailund did. Though he wasn’t explicit either, so whatever conclusions you draw are your own. But perhaps a reminder that when people are talking about things in public that might seem curious or a bit farther than the evidence warrants, it may be an issue of you not knowing what they know.

Why Belief in God Is Not Innate. I think the author is trying too hard, playing shell games with various types of non-Christianity. Unfortunately this area is dominated by pro and anti religious polemicists who wish to promote a strong and exclusive form of their prediction.

Complexity and Diversity. Frequency dependence is critical in maintaining variation on the intra and inter species level. Economists aren’t the only ones who need to move beyond equilibrium thinking.

Equalizing standardized test scores I assume everyone knows that at elite universities there’s an Asian penalty, and blacks and Hispanics tend to get a bonus, with whites as a reference population in the middle. The author warned though that looking at standardized test scores may not indicate any discrimination against Asians, as it didn’t include in other “soft” aspects of the application such as leadership, which Asians naturally must lack because of their conformist and collectivist nature (OK, I added the last part!). But the class chart was more interesting to me….

It looks like you better not be too dumb if you’re middle class. Lower class people get a nice handicap, while presumably the low scoring upper class types are stereotypical legacies. But at elite universities if you’re of middle socioeconomic status I guess all the leadership and exceptional talents can’t help; acceptance rates ~0 once your SAT scores approach the national norm.

But is this a matter of the confounds? In other words is this is a real signal of class based discrimination, or are there differences in the makeup of each class demographically skewing this? Here’s a regression model which seems to suggest there isn’t much to class, but more to race. The blacks in this case are broken down between descendants of slaves, and those who are presumably the children of immigrants or immigrants from the West Indies and Africa.

The racial effects are the ones which are statistically significant. It’s interesting that black Americans who don’t have any recent immigrant ancestry get a very significant boost vis-a-vis West Indians, etc.

Several people have pointed me to Stephen Hawking’s warning about ‘First Contact’ with aliens. Specifically that we’d be on the short end of the stick. His worry reminded me of something I read as a child which shocked me somewhat when I encountered it, as I was conditioned by a post-Cosmos optimism. Here’s the author:

…I find it mind-boggling that the astronomers now eager to spend a hundred million dollars on the search for extraterrestrial life never thought seriously about the most obvious question: what would happen if we found it, or if it found us. The astronomers tacitly assume that we and the little green monsters would welcome each other and settle down to fascinating conversations. Here again, our own experience on Earth offers useful guidance. We’ve already discovered two species that are very itnelligent but less technically advanced than we are-the common chimpanzee and pygmy chimpanzee. Has our response been to sit down and try to communicate with them? Of course not. Instead we shoot them, dissect them, cut off their hands for trophies, put them on exhibit in cages, inject them with AIDS virus as a medical experiment, and estroy or take over their habitats. That response was predictable, because human explorers who discvered technically less advanced humans also regularly responded by shooting them, decimating their popualtiosn with new diseases, and destroything or taking over their habitats.

Any advanced extraterrestrials who discovered us would surely treat us in the same way….

That was Jared Diamond in The Third Chimpanzee. In terms of this particular concern I have to admit that my attitude is encapsulated by Arthur C. Clarke’s third law of prediction. An advanced alien race is basically going to have magical powers in relation to humanity, and I doubt anything we do will matter either way (i.e., I don’t think we could hide, or, get their attention). But my main question is why haven’t the von Neumann machines already co-opted all the matter and energy in the universe? The Fermi paradox is a real issue. There are still big questions that we have no idea or clue about.

Michael Arrington of TechCrunch has a post up, The Age Of Facebook. Facebook having superseded Google having superseded Microsoft. Unstated that Microsoft superseded IBM as a firm which defines an age through reach, power and influence. Two thoughts that come to mind:

1) It seems that each “age” has been shorter than the previous. IBM was computing for decades. Microsoft probably ten years or so depending on how you define it (I put the second derivate maximum at 1995). Google’s real ascent seems to date to around 2000, but its monopolistic plateau of the mindshare didn’t seem to last for very long as Facebook was already generating a lot of buzz by 2007 (the same principle operates across human history, the civilization of Pharaonic Egypt spanned 2,000 years, the same length as from Augustus to our own time!)

2) It also seems that the extent of a definite age of ascendancy for a particular firm is more muddled now, as creative destruction and innovation allow for many domains of excellence and supremacy, as well as the resurrection of bygone brands. Consider the revival of Apple’s fortunes. And if we are on the verge of the Age of Facebook does anyone believe that Google’s brand will collapse? Arrington notes that Microsoft is perceived to be passed its peak, but it has many years left of its cash cow products, perhaps at least another decade. IBM has reemerged as a software services company. And so on. On a relative scale Arrington’s argument seems to have some merit, but secure domination doesn’t seem to be what it used to be (also, one might need to distinguish between buzz and influence, and concrete metrics).